/*
 *
 *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
 *
 *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman and Sebastian Böcker,
 *  Chair of Bioinformatics, Friedrich-Schilller University.
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 3 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
 */

package de.unijena.bionf.spectral_alignment;

import de.unijena.bioinf.ChemistryBase.ms.Deviation;
import de.unijena.bioinf.ChemistryBase.ms.Peak;
import de.unijena.bioinf.ChemistryBase.ms.utils.OrderedSpectrum;

/**
 * spectral comparison. dot product like.
 */
public abstract class AbstractSpectralMatching {

    protected final Deviation deviation;

    /**
     * @param deviation should be higher than usual expected mass deviation to not punish mz errors too much. this results in low cosine scores even for the same compounds
     */
    public AbstractSpectralMatching(Deviation deviation) {
        this.deviation = deviation;
    }

    public abstract SpectralSimilarity score(OrderedSpectrum<Peak> left, OrderedSpectrum<Peak> right, double precursorLeft, double precursorRight);
}
